Starting phenix.real_space_refine
on Thu Jun 12 10:43:30 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7qds_13925/06_2025/7qds_13925.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qds_13925/06_2025/7qds_13925.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qds_13925/06_2025/7qds_13925.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qds_13925/06_2025/7qds_13925.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qds_13925/06_2025/7qds_13925.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qds_13925/06_2025/7qds_13925.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      60      5.16       5
     C    8774      2.51       5
     N    2355      2.21       5
     O    2609      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 82 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13798
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 155, 1192
          Classifications: {'peptide': 155}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 20, 'TRANS': 134}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 28
          Unresolved non-hydrogen dihedrals: 16
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 7860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1006, 7860
          Classifications: {'peptide': 1006}
          Link IDs: {'PTRANS': 24, 'TRANS': 981}
    Chain: "C"
      Number of atoms: 2373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2373
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 8, 'TRANS': 296}
    Chain: "D"
      Number of atoms: 2373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 305, 2373
          Classifications: {'peptide': 305}
          Link IDs: {'PTRANS': 8, 'TRANS': 296}
  Time building chain proxies: 8.07, per 1000 atoms: 0.58
  Number of scatterers: 13798
  At special positions: 0
  Unit cell: (145.502, 117.058, 122.528, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      60     16.00
     O    2609      8.00
     N    2355      7.00
     C    8774      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.24
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3320

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 18 sheets defined
      48.6% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 53 through 64
    Processing helix  chain 'A' and resid 69 through 73
      removed outlier: 3.813A  pdb=" N   GLY A  73 " --> pdb=" O   PRO A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 91
      removed outlier: 3.578A  pdb=" N   LEU A  90 " --> pdb=" O   PRO A  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 563 through 577
      removed outlier: 3.548A  pdb=" N   ARG B 569 " --> pdb=" O   TRP B 565 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ALA B 577 " --> pdb=" O   TYR B 573 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 579 through 594
    Processing helix  chain 'B' and resid 597 through 611
      removed outlier: 3.616A  pdb=" N   ARG B 611 " --> pdb=" O   ALA B 607 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 614 through 627
      removed outlier: 3.988A  pdb=" N   LEU B 627 " --> pdb=" O   LYS B 623 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 645
      removed outlier: 3.627A  pdb=" N   VAL B 635 " --> pdb=" O   SER B 631 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   LEU B 645 " --> pdb=" O   ILE B 641 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 647 through 662
      removed outlier: 3.695A  pdb=" N   ALA B 651 " --> pdb=" O   LYS B 647 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 686
      removed outlier: 3.580A  pdb=" N   ASP B 686 " --> pdb=" O   ALA B 682 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 710
      removed outlier: 3.936A  pdb=" N   HIS B 709 " --> pdb=" O   CYS B 705 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ARG B 710 " --> pdb=" O   ALA B 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 726
      removed outlier: 4.302A  pdb=" N   TRP B 717 " --> pdb=" O   VAL B 713 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 741 through 745
      removed outlier: 3.586A  pdb=" N   LEU B 744 " --> pdb=" O   GLY B 741 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 754 through 773
      removed outlier: 3.954A  pdb=" N   LEU B 772 " --> pdb=" O   ARG B 768 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   MET B 773 " --> pdb=" O   ALA B 769 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 775 through 796
    Processing helix  chain 'B' and resid 803 through 821
    Processing helix  chain 'B' and resid 824 through 836
      removed outlier: 3.731A  pdb=" N   TRP B 828 " --> pdb=" O   ASN B 824 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   CYS B 836 " --> pdb=" O   GLY B 832 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 842 through 857
    Processing helix  chain 'B' and resid 860 through 874
      removed outlier: 3.819A  pdb=" N   TRP B 864 " --> pdb=" O   ASN B 860 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 876 through 891
    Processing helix  chain 'B' and resid 894 through 908
      removed outlier: 3.915A  pdb=" N   TRP B 898 " --> pdb=" O   TYR B 894 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 912 through 925
      removed outlier: 3.610A  pdb=" N   ASN B 924 " --> pdb=" O   THR B 920 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   MET B 925 " --> pdb=" O   THR B 921 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 926 through 943
    Processing helix  chain 'B' and resid 951 through 960
    Processing helix  chain 'B' and resid 960 through 976
      removed outlier: 3.613A  pdb=" N   ALA B 964 " --> pdb=" O   ASN B 960 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 979 through 993
      removed outlier: 3.803A  pdb=" N   PHE B 983 " --> pdb=" O   TYR B 979 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 995 through 1011
      removed outlier: 3.506A  pdb=" N   ALA B 999 " --> pdb=" O   LEU B 995 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1019 through 1033
      removed outlier: 3.591A  pdb=" N   THR B1033 " --> pdb=" O   LEU B1029 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1035 through 1045
    Processing helix  chain 'B' and resid 1050 through 1065
    Processing helix  chain 'B' and resid 1066 through 1080
      removed outlier: 3.738A  pdb=" N   ILE B1080 " --> pdb=" O   ARG B1076 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1084 through 1101
      removed outlier: 3.853A  pdb=" N   GLN B1101 " --> pdb=" O   THR B1097 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1103 through 1116
      removed outlier: 3.746A  pdb=" N   ALA B1107 " --> pdb=" O   LYS B1103 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1123 through 1134
    Processing helix  chain 'B' and resid 1139 through 1152
      removed outlier: 3.813A  pdb=" N   HIS B1151 " --> pdb=" O   GLU B1147 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE B1152 " --> pdb=" O   LEU B1148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1159 through 1172
      removed outlier: 3.724A  pdb=" N   GLN B1172 " --> pdb=" O   ILE B1168 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1176 through 1189
      removed outlier: 3.557A  pdb=" N   LYS B1180 " --> pdb=" O   VAL B1176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1192 through 1206
      removed outlier: 3.853A  pdb=" N   TRP B1196 " --> pdb=" O   ASP B1192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1210 through 1224
    Processing helix  chain 'B' and resid 1228 through 1244
    Processing helix  chain 'B' and resid 1254 through 1266
    Processing helix  chain 'B' and resid 1269 through 1291
      removed outlier: 4.494A  pdb=" N   TRP B1273 " --> pdb=" O   ASP B1269 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ALA B1274 " --> pdb=" O   PRO B1270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1299 through 1313
      removed outlier: 4.126A  pdb=" N   ASP B1313 " --> pdb=" O   ALA B1309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1317 through 1340
    Processing helix  chain 'B' and resid 1341 through 1356
      removed outlier: 3.648A  pdb=" N   ASN B1356 " --> pdb=" O   ASN B1352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1359 through 1371
      removed outlier: 3.715A  pdb=" N   ILE B1363 " --> pdb=" O   GLN B1359 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   LEU B1364 " --> pdb=" O   PRO B1360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1382 through 1396
    Processing helix  chain 'B' and resid 1399 through 1414
      removed outlier: 3.844A  pdb=" N   TRP B1403 " --> pdb=" O   SER B1399 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1415 through 1434
    Processing helix  chain 'B' and resid 1436 through 1456
      removed outlier: 4.028A  pdb=" N   ALA B1456 " --> pdb=" O   LYS B1452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1462 through 1478
    Processing helix  chain 'B' and resid 1480 through 1494
    Processing helix  chain 'B' and resid 1499 through 1511
    Processing helix  chain 'B' and resid 1515 through 1533
    Processing helix  chain 'B' and resid 1535 through 1548
    Processing helix  chain 'B' and resid 1552 through 1563
      removed outlier: 4.089A  pdb=" N   SER B1563 " --> pdb=" O   GLN B1559 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23
    Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104
    Processing sheet with id=AA3, first strand: chain 'B' and resid 737 through 739
    Processing sheet with id=AA4, first strand: chain 'C' and resid 6 through 11
      removed outlier: 7.039A  pdb=" N   ILE C 300 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   LYS C  10 " --> pdb=" O   ILE C 298 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ILE C 298 " --> pdb=" O   LYS C  10 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 25
      removed outlier: 6.563A  pdb=" N   VAL C  46 " --> pdb=" O   GLN C  57 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 67 through 72
      removed outlier: 3.515A  pdb=" N   SER C  69 " --> pdb=" O   SER C  82 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   ALA C  79 " --> pdb=" O   TRP C  91 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 112 through 113
      removed outlier: 3.752A  pdb=" N   TYR C 142 " --> pdb=" O   ILE C 132 " (cutoff:3.500A)
      removed outlier: 7.078A  pdb=" N   GLY C 134 " --> pdb=" O   LYS C 140 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   LYS C 140 " --> pdb=" O   GLY C 134 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 151 through 156
      removed outlier: 6.630A  pdb=" N   GLY C 166 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ILE C 154 " --> pdb=" O   ALA C 164 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ALA C 164 " --> pdb=" O   ILE C 154 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ILE C 174 " --> pdb=" O   HIS C 184 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   HIS C 184 " --> pdb=" O   ILE C 174 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 196 through 198
    Processing sheet with id=AB1, first strand: chain 'C' and resid 213 through 217
      removed outlier: 6.073A  pdb=" N   ILE C 214 " --> pdb=" O   THR C 227 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   THR C 227 " --> pdb=" O   ILE C 214 " (cutoff:3.500A)
      removed outlier: 6.177A  pdb=" N   ILE C 216 " --> pdb=" O   ALA C 225 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 235 through 240
      removed outlier: 3.550A  pdb=" N   ASN C 237 " --> pdb=" O   SER C 250 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   HIS C 268 " --> pdb=" O   VAL C 258 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   ASP C 260 " --> pdb=" O   CYS C 266 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   CYS C 266 " --> pdb=" O   ASP C 260 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 21 through 25
      removed outlier: 3.714A  pdb=" N   TRP D  58 " --> pdb=" O   VAL D  46 " (cutoff:3.500A)
      removed outlier: 6.539A  pdb=" N   LYS D  48 " --> pdb=" O   LEU D  56 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   LEU D  56 " --> pdb=" O   LYS D  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 67 through 72
      removed outlier: 3.506A  pdb=" N   SER D  69 " --> pdb=" O   SER D  82 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   LYS D 100 " --> pdb=" O   LEU D  90 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 112 through 113
    Processing sheet with id=AB6, first strand: chain 'D' and resid 163 through 166
      removed outlier: 3.825A  pdb=" N   ILE D 174 " --> pdb=" O   HIS D 184 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   HIS D 184 " --> pdb=" O   ILE D 174 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 195 through 197
      removed outlier: 4.569A  pdb=" N   SER D 195 " --> pdb=" O   ALA D 208 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ILE D 216 " --> pdb=" O   GLY D 226 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLY D 226 " --> pdb=" O   ILE D 216 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 235 through 239
      removed outlier: 6.835A  pdb=" N   SER D 250 " --> pdb=" O   LEU D 236 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   VAL D 238 " --> pdb=" O   VAL D 248 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   VAL D 248 " --> pdb=" O   VAL D 238 " (cutoff:3.500A)
      removed outlier: 4.566A  pdb=" N   SER D 255 " --> pdb=" O   SER D 251 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   VAL D 256 " --> pdb=" O   PHE D 270 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   HIS D 268 " --> pdb=" O   VAL D 258 " (cutoff:3.500A)
      removed outlier: 7.088A  pdb=" N   ASP D 260 " --> pdb=" O   CYS D 266 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   CYS D 266 " --> pdb=" O   ASP D 260 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'D' and resid 277 through 282

    714 hydrogen bonds defined for protein.
    2067 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.58

  Time building geometry restraints manager: 3.84 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 4467
        1.34 -     1.46: 2215
        1.46 -     1.58: 7327
        1.58 -     1.69: 0
        1.69 -     1.81: 88
  Bond restraints: 14097
  Sorted by residual:
  bond pdb=" CB  VAL D 290 "
       pdb=" CG2 VAL D 290 "
    ideal  model  delta    sigma   weight residual
    1.521  1.465  0.056 3.30e-02 9.18e+02 2.85e+00
  bond pdb=" CB  ILE B 968 "
       pdb=" CG2 ILE B 968 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.35e+00
  bond pdb=" CB  GLU A  31 "
       pdb=" CG  GLU A  31 "
    ideal  model  delta    sigma   weight residual
    1.520  1.479  0.041 3.00e-02 1.11e+03 1.87e+00
  bond pdb=" CB  CYS B 715 "
       pdb=" SG  CYS B 715 "
    ideal  model  delta    sigma   weight residual
    1.808  1.767  0.041 3.30e-02 9.18e+02 1.52e+00
  bond pdb=" CG1 ILE B1007 "
       pdb=" CD1 ILE B1007 "
    ideal  model  delta    sigma   weight residual
    1.513  1.469  0.044 3.90e-02 6.57e+02 1.29e+00
  ... (remaining 14092 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.48: 18961
        3.48 -     6.97: 166
        6.97 -    10.45: 11
       10.45 -    13.93: 2
       13.93 -    17.42: 1
  Bond angle restraints: 19141
  Sorted by residual:
  angle pdb=" C   GLU A  31 "
        pdb=" CA  GLU A  31 "
        pdb=" CB  GLU A  31 "
      ideal   model   delta    sigma   weight residual
     110.67  120.27   -9.60 2.23e+00 2.01e-01 1.85e+01
  angle pdb=" CA  LEU A  43 "
        pdb=" CB  LEU A  43 "
        pdb=" CG  LEU A  43 "
      ideal   model   delta    sigma   weight residual
     116.30  129.46  -13.16 3.50e+00 8.16e-02 1.41e+01
  angle pdb=" CB  MET A 194 "
        pdb=" CG  MET A 194 "
        pdb=" SD  MET A 194 "
      ideal   model   delta    sigma   weight residual
     112.70  101.54   11.16 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" C   GLU B1014 "
        pdb=" N   ASP B1015 "
        pdb=" CA  ASP B1015 "
      ideal   model   delta    sigma   weight residual
     125.66  132.08   -6.42 1.85e+00 2.92e-01 1.20e+01
  angle pdb=" N   GLU A  31 "
        pdb=" CA  GLU A  31 "
        pdb=" CB  GLU A  31 "
      ideal   model   delta    sigma   weight residual
     111.62  106.47    5.15 1.62e+00 3.81e-01 1.01e+01
  ... (remaining 19136 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.33: 7445
       17.33 -    34.65: 816
       34.65 -    51.98: 112
       51.98 -    69.31: 22
       69.31 -    86.63: 18
  Dihedral angle restraints: 8413
    sinusoidal: 3260
      harmonic: 5153
  Sorted by residual:
  dihedral pdb=" CA  ASP D 201 "
           pdb=" C   ASP D 201 "
           pdb=" N   SER D 202 "
           pdb=" CA  SER D 202 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -152.83  -27.17     0      5.00e+00 4.00e-02 2.95e+01
  dihedral pdb=" CA  ARG B 947 "
           pdb=" C   ARG B 947 "
           pdb=" N   GLU B 948 "
           pdb=" CA  GLU B 948 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.25   25.75     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  GLY D  38 "
           pdb=" C   GLY D  38 "
           pdb=" N   SER D  39 "
           pdb=" CA  SER D  39 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.56  -25.44     0      5.00e+00 4.00e-02 2.59e+01
  ... (remaining 8410 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1406
       0.042 -    0.084: 557
       0.084 -    0.125: 161
       0.125 -    0.167: 32
       0.167 -    0.209: 6
  Chirality restraints: 2162
  Sorted by residual:
  chirality pdb=" CB  ILE D 151 "
            pdb=" CA  ILE D 151 "
            pdb=" CG1 ILE D 151 "
            pdb=" CG2 ILE D 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CA  GLU A  31 "
            pdb=" N   GLU A  31 "
            pdb=" C   GLU A  31 "
            pdb=" CB  GLU A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.05e-01
  chirality pdb=" CA  ASN B1396 "
            pdb=" N   ASN B1396 "
            pdb=" C   ASN B1396 "
            pdb=" CB  ASN B1396 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.67e-01
  ... (remaining 2159 not shown)

  Planarity restraints: 2434
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B1119 "    0.092 5.00e-02 4.00e+02   1.39e-01 3.07e+01
        pdb=" N   PRO B1120 "   -0.240 5.00e-02 4.00e+02
        pdb=" CA  PRO B1120 "    0.076 5.00e-02 4.00e+02
        pdb=" CD  PRO B1120 "    0.071 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C 105 "   -0.048 5.00e-02 4.00e+02   7.37e-02 8.70e+00
        pdb=" N   PRO C 106 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO C 106 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO C 106 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B1256 "    0.015 2.00e-02 2.50e+03   2.90e-02 8.43e+00
        pdb=" C   LEU B1256 "   -0.050 2.00e-02 2.50e+03
        pdb=" O   LEU B1256 "    0.019 2.00e-02 2.50e+03
        pdb=" N   LYS B1257 "    0.017 2.00e-02 2.50e+03
  ... (remaining 2431 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 207
        2.63 -     3.20: 13015
        3.20 -     3.77: 20682
        3.77 -     4.33: 27067
        4.33 -     4.90: 46078
  Nonbonded interactions: 107049
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 251 "
            pdb=" OD1 ASP C 253 "
     model   vdw
     2.067 3.040
  nonbonded pdb=" OE2 GLU B1314 "
            pdb=" ND2 ASN B1321 "
     model   vdw
     2.094 3.120
  nonbonded pdb=" OG  SER B1157 "
            pdb=" OE1 GLN B1160 "
     model   vdw
     2.108 3.040
  nonbonded pdb=" OD1 ASP D 253 "
            pdb=" OG  SER D 255 "
     model   vdw
     2.172 3.040
  nonbonded pdb=" OE1 GLN B 588 "
            pdb=" OH  TYR B 608 "
     model   vdw
     2.188 3.040
  ... (remaining 107044 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.490
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     31.730
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.000
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  14097  Z= 0.202
  Angle     :  0.856  17.416  19141  Z= 0.456
  Chirality :  0.049   0.209   2162
  Planarity :  0.006   0.139   2434
  Dihedral  : 14.594  86.633   5093
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.33 (0.21), residues: 1761
  helix:  2.76 (0.18), residues: 806
  sheet: -1.96 (0.31), residues: 250
  loop : -3.37 (0.18), residues: 705

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP B 936 
 HIS   0.013   0.002   HIS B 992 
 PHE   0.029   0.003   PHE D 240 
 TYR   0.034   0.002   TYR D 156 
 ARG   0.007   0.001   ARG B1553 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13418 (  714)
  hydrogen bonds       : angle       5.45123 ( 2067)
  covalent geometry    : bond        0.00465 (14097)
  covalent geometry    : angle       0.85647 (19141)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 1.464 
Fit side-chains
REVERT: A  192 LYS cc_start: 0.8440 (mttt) cc_final: 0.8177 (tttp)
REVERT: B 1118 LYS cc_start: 0.7763 (pptt) cc_final: 0.7221 (mmtt)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.2418
  time to fit residues: 45.5269
Evaluate side-chains
  82 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 1.592 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 147 optimal weight:    0.9990
   chunk 132 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 89 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 137 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 83 optimal weight:    0.2980
   chunk 102 optimal weight:    0.0020
   chunk 158 optimal weight:    0.5980
   overall best weight:    0.4388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 588 GLN
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.114297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.088570 restraints weight = 27819.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.089348 restraints weight = 20774.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.090612 restraints weight = 16576.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14097  Z= 0.137
  Angle     :  0.667  11.775  19141  Z= 0.344
  Chirality :  0.043   0.168   2162
  Planarity :  0.005   0.080   2434
  Dihedral  :  5.135  23.939   1886
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  :  9.65 %
    Favored  : 89.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.21), residues: 1761
  helix:  2.56 (0.18), residues: 828
  sheet: -1.57 (0.33), residues: 243
  loop : -3.11 (0.19), residues: 690

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 936 
 HIS   0.004   0.001   HIS B1187 
 PHE   0.021   0.002   PHE D 240 
 TYR   0.019   0.001   TYR B 935 
 ARG   0.005   0.000   ARG B1005 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04401 (  714)
  hydrogen bonds       : angle       4.28819 ( 2067)
  covalent geometry    : bond        0.00297 (14097)
  covalent geometry    : angle       0.66746 (19141)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 1.511 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 GLU cc_start: 0.7160 (tp30) cc_final: 0.6847 (tp30)
REVERT: A  192 LYS cc_start: 0.8386 (mttt) cc_final: 0.8185 (tttp)
REVERT: B 1118 LYS cc_start: 0.7695 (pptt) cc_final: 0.6975 (mmtt)
REVERT: B 1383 ASP cc_start: 0.8341 (OUTLIER) cc_final: 0.8083 (t0)
  outliers start: 14
  outliers final: 5
  residues processed: 132
  average time/residue: 0.2384
  time to fit residues: 49.0611
Evaluate side-chains
  95 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 1.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain B residue 1116 ILE
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain D residue  201 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 134 optimal weight:    1.9990
   chunk 143 optimal weight:    0.9980
   chunk 137 optimal weight:    3.9990
   chunk 171 optimal weight:    0.5980
   chunk 19 optimal weight:    5.9990
   chunk 138 optimal weight:    0.7980
   chunk 158 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 152 optimal weight:    3.9990
   chunk 140 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 642 GLN
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1321 ASN
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.110378 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.085223 restraints weight = 28149.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.085704 restraints weight = 22492.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.086504 restraints weight = 19322.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.1563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14097  Z= 0.173
  Angle     :  0.656  11.305  19141  Z= 0.342
  Chirality :  0.043   0.167   2162
  Planarity :  0.005   0.059   2434
  Dihedral  :  5.108  25.381   1886
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 12.62 %
    Favored  : 85.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.21), residues: 1761
  helix:  2.43 (0.18), residues: 829
  sheet: -1.44 (0.33), residues: 256
  loop : -3.10 (0.20), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 936 
 HIS   0.004   0.001   HIS C 189 
 PHE   0.022   0.002   PHE B1316 
 TYR   0.014   0.001   TYR B 935 
 ARG   0.004   0.000   ARG B1005 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04586 (  714)
  hydrogen bonds       : angle       4.13321 ( 2067)
  covalent geometry    : bond        0.00401 (14097)
  covalent geometry    : angle       0.65609 (19141)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 103
  time to evaluate  : 1.516 
Fit side-chains
REVERT: A  192 LYS cc_start: 0.8397 (mttt) cc_final: 0.8197 (tttt)
REVERT: B 1383 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8054 (t0)
REVERT: D   94 GLU cc_start: 0.7898 (tp30) cc_final: 0.7525 (tp30)
  outliers start: 35
  outliers final: 18
  residues processed: 134
  average time/residue: 0.2144
  time to fit residues: 46.9347
Evaluate side-chains
  111 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 1.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain B residue 1116 ILE
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1310 SER
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue   70 VAL
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  250 SER
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain D residue  153 SER
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 159 optimal weight:    0.7980
   chunk 54 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 104 optimal weight:    0.5980
   chunk 100 optimal weight:    0.8980
   chunk 128 optimal weight:    0.9990
   chunk 88 optimal weight:    0.0870
   chunk 91 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.6358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 942 GLN
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.111515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.086499 restraints weight = 27880.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.086534 restraints weight = 21613.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.087150 restraints weight = 18801.226|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14097  Z= 0.132
  Angle     :  0.610  15.687  19141  Z= 0.314
  Chirality :  0.042   0.167   2162
  Planarity :  0.004   0.052   2434
  Dihedral  :  4.884  22.600   1886
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.24 %
    Favored  : 83.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.21), residues: 1761
  helix:  2.47 (0.18), residues: 829
  sheet: -1.29 (0.34), residues: 262
  loop : -2.98 (0.20), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  47 
 HIS   0.003   0.001   HIS D  15 
 PHE   0.013   0.001   PHE D 150 
 TYR   0.013   0.001   TYR B 935 
 ARG   0.003   0.000   ARG B1005 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03904 (  714)
  hydrogen bonds       : angle       3.91073 ( 2067)
  covalent geometry    : bond        0.00296 (14097)
  covalent geometry    : angle       0.60995 (19141)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 108
  time to evaluate  : 1.566 
Fit side-chains
REVERT: A  192 LYS cc_start: 0.8423 (mttt) cc_final: 0.8203 (tttt)
REVERT: B 1118 LYS cc_start: 0.7661 (pptt) cc_final: 0.6823 (mmtt)
REVERT: B 1383 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.8125 (t0)
REVERT: B 1504 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8061 (tp)
REVERT: D   94 GLU cc_start: 0.7874 (tp30) cc_final: 0.7544 (tp30)
  outliers start: 36
  outliers final: 19
  residues processed: 138
  average time/residue: 0.2199
  time to fit residues: 48.7693
Evaluate side-chains
  113 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 1.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  722 ASP
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1098 GLU
Chi-restraints excluded: chain B residue 1116 ILE
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1504 LEU
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  250 SER
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 141 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   chunk 11 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.110103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.084857 restraints weight = 28248.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.085357 restraints weight = 22438.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.086300 restraints weight = 18240.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14097  Z= 0.151
  Angle     :  0.619  13.270  19141  Z= 0.319
  Chirality :  0.042   0.166   2162
  Planarity :  0.004   0.047   2434
  Dihedral  :  4.856  23.824   1886
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 15.92 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.21), residues: 1761
  helix:  2.48 (0.18), residues: 829
  sheet: -1.31 (0.34), residues: 256
  loop : -3.00 (0.20), residues: 676

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 259 
 HIS   0.004   0.001   HIS C 126 
 PHE   0.024   0.002   PHE B1316 
 TYR   0.012   0.001   TYR B 935 
 ARG   0.002   0.000   ARG B1005 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04090 (  714)
  hydrogen bonds       : angle       3.88087 ( 2067)
  covalent geometry    : bond        0.00348 (14097)
  covalent geometry    : angle       0.61889 (19141)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 101
  time to evaluate  : 1.499 
Fit side-chains
REVERT: A  192 LYS cc_start: 0.8411 (mttt) cc_final: 0.8206 (tttt)
REVERT: B 1101 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.8046 (mt0)
REVERT: B 1118 LYS cc_start: 0.7677 (pptt) cc_final: 0.6778 (mmtt)
REVERT: B 1383 ASP cc_start: 0.8330 (OUTLIER) cc_final: 0.8068 (t0)
REVERT: B 1504 LEU cc_start: 0.8169 (OUTLIER) cc_final: 0.7957 (tp)
REVERT: C  241 CYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8535 (t)
REVERT: D   94 GLU cc_start: 0.7983 (tp30) cc_final: 0.7609 (tp30)
  outliers start: 43
  outliers final: 27
  residues processed: 141
  average time/residue: 0.2231
  time to fit residues: 50.5900
Evaluate side-chains
  127 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 96
  time to evaluate  : 1.608 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1101 GLN
Chi-restraints excluded: chain B residue 1116 ILE
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1272 ILE
Chi-restraints excluded: chain B residue 1310 SER
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1504 LEU
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  250 SER
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain D residue   58 TRP
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  153 SER
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 154 optimal weight:    0.1980
   chunk 146 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 108 optimal weight:    0.4980
   chunk 50 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 131 optimal weight:    0.7980
   chunk 153 optimal weight:    1.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B1146 ASN
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1491 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.108709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.083636 restraints weight = 28601.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.084096 restraints weight = 24533.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.084743 restraints weight = 20123.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  14097  Z= 0.175
  Angle     :  0.636  12.802  19141  Z= 0.330
  Chirality :  0.043   0.168   2162
  Planarity :  0.004   0.049   2434
  Dihedral  :  4.907  24.113   1886
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.34 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 16.94 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.21), residues: 1761
  helix:  2.44 (0.18), residues: 829
  sheet: -1.34 (0.34), residues: 255
  loop : -3.02 (0.20), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP D  47 
 HIS   0.004   0.001   HIS C 126 
 PHE   0.016   0.002   PHE D 150 
 TYR   0.012   0.001   TYR B 935 
 ARG   0.004   0.000   ARG B1502 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04353 (  714)
  hydrogen bonds       : angle       3.90792 ( 2067)
  covalent geometry    : bond        0.00407 (14097)
  covalent geometry    : angle       0.63565 (19141)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 101
  time to evaluate  : 1.757 
Fit side-chains
   revert: symmetry clash
REVERT: A  192 LYS cc_start: 0.8429 (mttt) cc_final: 0.8174 (tttt)
REVERT: B  773 MET cc_start: 0.8169 (mmm) cc_final: 0.7869 (mmm)
REVERT: B 1101 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7903 (mt0)
REVERT: B 1118 LYS cc_start: 0.7739 (pptt) cc_final: 0.6827 (mmtt)
REVERT: B 1383 ASP cc_start: 0.8347 (OUTLIER) cc_final: 0.8095 (t0)
REVERT: B 1504 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8085 (tp)
REVERT: D   94 GLU cc_start: 0.7999 (tp30) cc_final: 0.7608 (tp30)
REVERT: D  156 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7456 (t80)
  outliers start: 44
  outliers final: 30
  residues processed: 142
  average time/residue: 0.2553
  time to fit residues: 57.5653
Evaluate side-chains
  126 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 92
  time to evaluate  : 1.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1101 GLN
Chi-restraints excluded: chain B residue 1116 ILE
Chi-restraints excluded: chain B residue 1160 GLN
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1272 ILE
Chi-restraints excluded: chain B residue 1310 SER
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1504 LEU
Chi-restraints excluded: chain B residue 1562 SER
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  250 SER
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain D residue   58 TRP
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  153 SER
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 157 optimal weight:    1.9990
   chunk 97 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 119 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 132 optimal weight:    0.5980
   chunk 108 optimal weight:    0.6980
   chunk 148 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 124 optimal weight:    0.0050
   overall best weight:    0.4994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.112703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.087487 restraints weight = 27889.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.088262 restraints weight = 21840.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.088992 restraints weight = 17511.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14097  Z= 0.122
  Angle     :  0.599  12.334  19141  Z= 0.308
  Chirality :  0.041   0.165   2162
  Planarity :  0.004   0.049   2434
  Dihedral  :  4.719  23.137   1886
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.31 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.68 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.21), residues: 1761
  helix:  2.52 (0.18), residues: 829
  sheet: -1.20 (0.34), residues: 251
  loop : -2.94 (0.20), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP D  47 
 HIS   0.006   0.001   HIS D  15 
 PHE   0.031   0.001   PHE B1316 
 TYR   0.011   0.001   TYR B 935 
 ARG   0.004   0.000   ARG B1503 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03614 (  714)
  hydrogen bonds       : angle       3.72863 ( 2067)
  covalent geometry    : bond        0.00272 (14097)
  covalent geometry    : angle       0.59865 (19141)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 102
  time to evaluate  : 1.508 
Fit side-chains
   revert: symmetry clash
REVERT: B  773 MET cc_start: 0.8188 (mmm) cc_final: 0.7821 (mmm)
REVERT: B  800 MET cc_start: 0.6011 (tpt) cc_final: 0.5434 (mmp)
REVERT: B 1101 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7893 (mt0)
REVERT: B 1118 LYS cc_start: 0.7572 (pptt) cc_final: 0.6738 (mmtt)
REVERT: B 1383 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8014 (t0)
REVERT: C  241 CYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8502 (t)
REVERT: D  156 TYR cc_start: 0.8144 (OUTLIER) cc_final: 0.7402 (t80)
  outliers start: 36
  outliers final: 24
  residues processed: 133
  average time/residue: 0.2149
  time to fit residues: 45.7703
Evaluate side-chains
  122 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 1.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1050 VAL
Chi-restraints excluded: chain B residue 1101 GLN
Chi-restraints excluded: chain B residue 1160 GLN
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1272 ILE
Chi-restraints excluded: chain B residue 1286 LEU
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1562 SER
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain D residue   58 TRP
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 174 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 80 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 50 optimal weight:    0.4980
   chunk 68 optimal weight:    2.9990
   chunk 172 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0670
   chunk 16 optimal weight:    9.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.5918

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.110319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.085110 restraints weight = 28201.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.085998 restraints weight = 21505.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.087205 restraints weight = 17077.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14097  Z= 0.127
  Angle     :  0.599  12.530  19141  Z= 0.309
  Chirality :  0.041   0.165   2162
  Planarity :  0.004   0.050   2434
  Dihedral  :  4.643  22.757   1886
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.82 %
    Favored  : 90.18 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 18.42 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.21), residues: 1761
  helix:  2.54 (0.18), residues: 829
  sheet: -1.13 (0.34), residues: 249
  loop : -2.91 (0.20), residues: 683

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP D  47 
 HIS   0.004   0.001   HIS C 126 
 PHE   0.013   0.001   PHE D 150 
 TYR   0.011   0.001   TYR B1536 
 ARG   0.003   0.000   ARG A   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03644 (  714)
  hydrogen bonds       : angle       3.69142 ( 2067)
  covalent geometry    : bond        0.00286 (14097)
  covalent geometry    : angle       0.59876 (19141)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 98
  time to evaluate  : 1.543 
Fit side-chains
   revert: symmetry clash
REVERT: B  773 MET cc_start: 0.8263 (mmm) cc_final: 0.7918 (mmm)
REVERT: B  800 MET cc_start: 0.5973 (tpt) cc_final: 0.5403 (mmp)
REVERT: B 1101 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7891 (mt0)
REVERT: B 1118 LYS cc_start: 0.7527 (pptt) cc_final: 0.6686 (mmtt)
REVERT: B 1383 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.8043 (t0)
REVERT: C  241 CYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8513 (t)
REVERT: D  156 TYR cc_start: 0.8161 (OUTLIER) cc_final: 0.7397 (t80)
  outliers start: 33
  outliers final: 26
  residues processed: 127
  average time/residue: 0.2357
  time to fit residues: 47.5548
Evaluate side-chains
  124 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 1.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1050 VAL
Chi-restraints excluded: chain B residue 1101 GLN
Chi-restraints excluded: chain B residue 1160 GLN
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1272 ILE
Chi-restraints excluded: chain B residue 1286 LEU
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1562 SER
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain D residue   58 TRP
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 172 optimal weight:    2.9990
   chunk 127 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 136 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0050
   chunk 166 optimal weight:    2.9990
   chunk 139 optimal weight:    0.7980
   chunk 115 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 121 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    0.5794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.110522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.085584 restraints weight = 27958.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.087041 restraints weight = 20757.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.087860 restraints weight = 16234.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14097  Z= 0.125
  Angle     :  0.599  12.888  19141  Z= 0.308
  Chirality :  0.041   0.164   2162
  Planarity :  0.004   0.050   2434
  Dihedral  :  4.596  22.970   1886
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.62 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.21), residues: 1761
  helix:  2.53 (0.18), residues: 831
  sheet: -1.15 (0.34), residues: 248
  loop : -2.85 (0.21), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP D  47 
 HIS   0.005   0.001   HIS D 126 
 PHE   0.013   0.001   PHE D 150 
 TYR   0.010   0.001   TYR B 935 
 ARG   0.006   0.000   ARG A   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03550 (  714)
  hydrogen bonds       : angle       3.65107 ( 2067)
  covalent geometry    : bond        0.00280 (14097)
  covalent geometry    : angle       0.59879 (19141)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 100
  time to evaluate  : 2.024 
Fit side-chains
   revert: symmetry clash
REVERT: B  773 MET cc_start: 0.8254 (mmm) cc_final: 0.7899 (mmm)
REVERT: B  800 MET cc_start: 0.5938 (tpt) cc_final: 0.5444 (mmp)
REVERT: B 1101 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7890 (mt0)
REVERT: B 1118 LYS cc_start: 0.7505 (pptt) cc_final: 0.6630 (mmtt)
REVERT: B 1140 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8232 (pp)
REVERT: B 1383 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.8043 (t0)
REVERT: B 1506 GLU cc_start: 0.7998 (pt0) cc_final: 0.7774 (pt0)
REVERT: C  241 CYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8581 (t)
REVERT: D  156 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7496 (t80)
  outliers start: 32
  outliers final: 25
  residues processed: 127
  average time/residue: 0.2659
  time to fit residues: 53.8429
Evaluate side-chains
  124 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 2.932 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1101 GLN
Chi-restraints excluded: chain B residue 1140 LEU
Chi-restraints excluded: chain B residue 1160 GLN
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1272 ILE
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1562 SER
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain D residue   58 TRP
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 158 optimal weight:    0.9990
   chunk 100 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9990
   chunk 103 optimal weight:    0.6980
   chunk 155 optimal weight:    0.0000
   chunk 111 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 144 optimal weight:    0.9980
   chunk 84 optimal weight:    0.6980
   overall best weight:    0.6786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.110082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.084761 restraints weight = 28247.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.086422 restraints weight = 21204.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.087006 restraints weight = 16816.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14097  Z= 0.134
  Angle     :  0.618  13.865  19141  Z= 0.316
  Chirality :  0.041   0.165   2162
  Planarity :  0.004   0.050   2434
  Dihedral  :  4.601  22.970   1886
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.88 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.76 %
    Favored  : 79.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.21), residues: 1761
  helix:  2.54 (0.18), residues: 830
  sheet: -1.17 (0.34), residues: 256
  loop : -2.81 (0.21), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP D  47 
 HIS   0.004   0.001   HIS C 126 
 PHE   0.014   0.001   PHE D 150 
 TYR   0.012   0.001   TYR B1536 
 ARG   0.006   0.000   ARG A   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03647 (  714)
  hydrogen bonds       : angle       3.65749 ( 2067)
  covalent geometry    : bond        0.00305 (14097)
  covalent geometry    : angle       0.61816 (19141)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3522 Ramachandran restraints generated.
    1761 Oldfield, 0 Emsley, 1761 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 95
  time to evaluate  : 1.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  773 MET cc_start: 0.8275 (mmm) cc_final: 0.7930 (mmm)
REVERT: B  800 MET cc_start: 0.5996 (tpt) cc_final: 0.5415 (mmp)
REVERT: B 1101 GLN cc_start: 0.8243 (OUTLIER) cc_final: 0.7903 (mt0)
REVERT: B 1118 LYS cc_start: 0.7489 (pptt) cc_final: 0.6777 (mmtt)
REVERT: B 1140 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8248 (pp)
REVERT: B 1383 ASP cc_start: 0.8351 (OUTLIER) cc_final: 0.8087 (t0)
REVERT: B 1506 GLU cc_start: 0.8077 (pt0) cc_final: 0.7848 (pt0)
REVERT: D  156 TYR cc_start: 0.8186 (OUTLIER) cc_final: 0.7420 (t80)
  outliers start: 32
  outliers final: 27
  residues processed: 122
  average time/residue: 0.2671
  time to fit residues: 52.1699
Evaluate side-chains
  125 residues out of total 1488 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 1.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain B residue  665 TYR
Chi-restraints excluded: chain B residue  803 LEU
Chi-restraints excluded: chain B residue  992 HIS
Chi-restraints excluded: chain B residue 1050 VAL
Chi-restraints excluded: chain B residue 1101 GLN
Chi-restraints excluded: chain B residue 1140 LEU
Chi-restraints excluded: chain B residue 1160 GLN
Chi-restraints excluded: chain B residue 1202 VAL
Chi-restraints excluded: chain B residue 1272 ILE
Chi-restraints excluded: chain B residue 1383 ASP
Chi-restraints excluded: chain B residue 1562 SER
Chi-restraints excluded: chain C residue   17 ASP
Chi-restraints excluded: chain C residue   67 VAL
Chi-restraints excluded: chain C residue  136 GLU
Chi-restraints excluded: chain C residue  146 THR
Chi-restraints excluded: chain C residue  168 ILE
Chi-restraints excluded: chain C residue  171 ILE
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  207 THR
Chi-restraints excluded: chain C residue  241 CYS
Chi-restraints excluded: chain C residue  258 VAL
Chi-restraints excluded: chain C residue  269 THR
Chi-restraints excluded: chain C residue  275 ASP
Chi-restraints excluded: chain D residue   58 TRP
Chi-restraints excluded: chain D residue   67 VAL
Chi-restraints excluded: chain D residue  123 THR
Chi-restraints excluded: chain D residue  154 ILE
Chi-restraints excluded: chain D residue  156 TYR
Chi-restraints excluded: chain D residue  238 VAL
Chi-restraints excluded: chain D residue  256 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 175
   random chunks:
   chunk 106 optimal weight:    0.8980
   chunk 93 optimal weight:    0.1980
   chunk 129 optimal weight:    0.3980
   chunk 150 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 71 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 140 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 12 optimal weight:    0.3980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** B1260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.111069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.085604 restraints weight = 28372.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.086424 restraints weight = 23795.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.087129 restraints weight = 18685.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  14097  Z= 0.123
  Angle     :  0.606  13.909  19141  Z= 0.310
  Chirality :  0.041   0.165   2162
  Planarity :  0.004   0.050   2434
  Dihedral  :  4.545  22.449   1886
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.71 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 18.62 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.21), residues: 1761
  helix:  2.55 (0.18), residues: 832
  sheet: -1.14 (0.34), residues: 255
  loop : -2.78 (0.21), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP D  47 
 HIS   0.005   0.001   HIS C 126 
 PHE   0.012   0.001   PHE D 150 
 TYR   0.010   0.001   TYR B 935 
 ARG   0.006   0.000   ARG A   6 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03442 (  714)
  hydrogen bonds       : angle       3.60312 ( 2067)
  covalent geometry    : bond        0.00275 (14097)
  covalent geometry    : angle       0.60565 (19141)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4507.68 seconds
wall clock time: 81 minutes 44.17 seconds (4904.17 seconds total)